Please run:
- namespaceDupes.php just to make sure that everything is alright
- refreshLinks.php with --dfn-only if needed to remove duplications (now that MediaWiki can fully convert Cyrillic -> Latin and vice versa)
- updateSpecialPages.php for MediaWiki to remove duplicates
- ... I don't think that there is anything more (see T185421 and feel free to come up with ideas)